September 2025 - Software - lists.biobrillouin.org

Presentation BioBrillouin
by Pierre Bouvet Sept. 30, 2025

Sept. 30, 2025

Hi everyone, I think it could be good to create either a presentation of our work together or even a roundtable session for the BioBrillouin conference. I believe the easiest to fit in the program is a standard presentation that we can call “Round table” so a 15 minute format. By default I would split the presentation as follows: A - Quick demonstration of work (7 minutes) 1 - How to create standard files from code a - Integration to workflow b - Adding attributes c - Exporting HDF5 elements to Brim 2 - How to create standard files form GUI 3 - How to view standard files in dedicated apps 4 - How to use unified treatment from code a - Simple example: DHO fit of spectrum from TFP b - Changing parameters c - Performances and errors between fit (motivation) B - Round table where people send everything they have at us AKA exchange with public (8 minutes) with a backup of identified difficulties in case people are asleep or not interested If you are OK with it, the best way to prepare for it would be to list the steps for using the apps with screen captures of results so we are sure we all get same result, and then decide on one computer with everything on it and that works well we could use for the presentation. Best, Pierre Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria

3 4

Fwd: arXiv New submission -> 2509.07566 in physics.optics from robert.prevedel@gmail.com
by Robert Prevedel Sept. 16, 2025

Sept. 16, 2025

Just in time!! Robert Begin forwarded message: > From: e-prints(a)arxiv.org > Date: 10. September 2025 at 02:06:19 WEST > To: robert.prevedel(a)gmail.com > Subject: arXiv New submission -> 2509.07566 in physics.optics from robert.prevedel(a)gmail.com > Reply-To: help(a)arxiv.org > > Your submission submit/6776954 has been assigned the permanent arXiv > identifier 2509.07566 and is available at: > > http://arxiv.org/abs/2509.07566 > > > The paper password for this article is: e7xqa > Please share this with your co-authors. They may use it to claim > ownership. > > > Abstract will appear in today's mailing as: > ------------------------------------------------------------------------------ > \\ > arXiv:2509.07566 > From: Robert Prevedel <robert.prevedel(a)gmail.com> > Date: Tue, 9 Sep 2025 10:07:44 GMT (1897kb) > > Title: A standardized file format and open-source analysis framework for > Brillouin microscopy data > Authors: Carlo Bevilacqua, Sebastian Hambura, Pierre Bouvet, Salvatore La > Cavera III, Kareem Elsayad and Robert Prevedel > Categories: physics.optics > Comments: 19 pages incl. Supplementary Information > License: http://creativecommons.org/licenses/by/4.0/ > \\ > Brillouin microscopy is rapidly emerging as a powerful technique for imaging > the mechanical properties of biological specimens in a label-free, non-contact > manner. We present a standardized file format and open-source tools to > facilitate the uptake and analysis of Brillouin microscopy related data and to > unify this growing field. > \\ > > > Contains: > Brillouin_file_format_paper_final_ArXiv.pdf: 1942774 bytes > >

3 4

Re: [EXTERN] Fwd: BIORXIV/2025/674600 -- Please Resubmit
by Kareem Elsayad Sept. 9, 2025

Sept. 9, 2025

Just occurred to me putting up on Zenodo might also be option? (from what I recall that goes almost instant and you get DOI) Quite funny they didn’t take (they rejected reviews by me before). Medarxiv can be even more picky (and funny), they wanted us once to replace “..a 25 year old woman..” with “a patient who identified as female between the age of 20 and 30…” so the reader cannot possibly identify the person. I mean who reads this and thinks “…you know that patient with the abnormal frequency-wavevector scaling of plasma viscosity in that pre-print? Well, that can only be Caroline from Tuesday Yoga class!” From: Kareem Elsayad <kareem.elsayad(a)meduniwien.ac.at> Date: Tuesday, 9. September 2025 at 11:45 To: Software Mailing list <software(a)biobrillouin.org> Subject: Re: [EXTERN] [Software] Fwd: BIORXIV/2025/674600 -- Please Resubmit Yes, I agree – let’s do arXiv then. From: Robert Prevedel via Software <software(a)biobrillouin.org> Reply to: Robert Prevedel <prevedel(a)embl.de> Date: Tuesday, 9. September 2025 at 10:06 To: Software Mailing list <software(a)biobrillouin.org> Subject: [EXTERN] [Software] Fwd: BIORXIV/2025/674600 -- Please Resubmit Dear all, please see below - surprisingly bioRxiv does not think our manuscript fits and they require more analysis/data. Shall we quickly submit to arXiv instead? Just let me know! Best, Robert -- Dr. Robert Prevedel Group Leader and Senior Scientist Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany Phone: +49 6221 387-8722 Email: robert.prevedel(a)embl.de http://www.prevedel.embl.de Begin forwarded message: From: bioRxiv(a)openrxiv.org Subject: BIORXIV/2025/674600 -- Please Resubmit Date: 9. September 2025 at 08:33:58 WEST To: prevedel(a)embl.de, prevedel(a)embl.de MS ID#: BIORXIV/2025/674600 MS TITLE: A standardized file format and open-source analysis framework for Brillouin microscopy data Dear Robert Prevedel; Thank you for submitting your manuscript to bioRxiv. bioRxiv is intended for complete research papers with new data/analysis rather than announcements of tools/resources/reagents and your submission falls into this category. We are, therefore, returning the manuscript to give you the opportunity to add analyses/data to support the utility of your tool/resource. This data can be added as supplemental information. If you decide to make these edits, please resupply your manuscript to the above manuscript ID BIORXIV/2025/674600. Please do not submit the manuscript as a new submission with a different manuscript ID number as this will delay screening. You will find this manuscript in the "Papers returned for your attention" section of your author area. Please contact us if you have any questions. The bioRxiv team _______________________________________________ Software mailing list -- software(a)biobrillouin.org To unsubscribe send an email to software-leave(a)biobrillouin.org

1 0

Fwd: BIORXIV/2025/674600 -- Please Resubmit
by Robert Prevedel Sept. 9, 2025

Sept. 9, 2025

Dear all, please see below - surprisingly bioRxiv does not think our manuscript fits and they require more analysis/data. Shall we quickly submit to arXiv instead? Just let me know! Best, Robert -- Dr. Robert Prevedel Group Leader and Senior Scientist Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany Phone: +49 6221 387-8722 Email: robert.prevedel(a)embl.de http://www.prevedel.embl.de > Begin forwarded message: > > From: bioRxiv(a)openrxiv.org > Subject: BIORXIV/2025/674600 -- Please Resubmit > Date: 9. September 2025 at 08:33:58 WEST > To: prevedel(a)embl.de, prevedel(a)embl.de > > MS ID#: BIORXIV/2025/674600 > MS TITLE: A standardized file format and open-source analysis framework for Brillouin microscopy data > > Dear Robert Prevedel; > > Thank you for submitting your manuscript to bioRxiv. bioRxiv is intended for complete research papers with new data/analysis rather than announcements of tools/resources/reagents and your submission falls into this category. We are, therefore, returning the manuscript to give you the opportunity to add analyses/data to support the utility of your tool/resource. This data can be added as supplemental information. > > If you decide to make these edits, please resupply your manuscript to the above manuscript ID BIORXIV/2025/674600. Please do not submit the manuscript as a new submission with a different manuscript ID number as this will delay screening. You will find this manuscript in the "Papers returned for your attention" section of your author area. Please contact us if you have any questions. > > The bioRxiv team

4 3

Paper preprint
by Robert Prevedel Sept. 7, 2025

Sept. 7, 2025

Dear all, as I understood, Pierre would appreciate a preprint being out before Sept. 10 for his grant application, and likelywise I’d be happy to see cite it in mine. This would mean we’d need to upload to e.g. bioRxiv by Monday evening the latest. Is everyone fine with this plan and ok given their state of code etc.? Also, please alert me of any last changes to the paper online in case you do any. Best, Robert -- Dr. Robert Prevedel Group Leader and Senior Scientist Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany Phone: +49 6221 387-8722 Email: robert.prevedel(a)embl.de http://www.prevedel.embl.de

5 8

Re: Newsletter
by Carlo Bevilacqua Sept. 4, 2025

Sept. 4, 2025

Hi Pierre, thanks for preparing the documents and sorry for the late reply, but we were finalizing the website in the past days. For the newsletter, I discussed with Robert and Sebastian and we would propose the attached paragraph. I attached also a PDF including my additions to the tutorial and I pushed the changes on the HDF5_BLS GitHub as well. To follow up on Robert's previous email, shall we have a meeting on Thursday 11th at 3pm? Best, Carlo On Thu, Sep 4, 2025 at 10:16, Pierre Bouvet wrote: Hi everyone, I’ll send the newsletter tomorrow, just want to make sure the message is OK. From what I understood, Carlo wanted to advertise more but Robert you preferred the first version? I’ve joined the capture of the paragraph dedicated to the file format. Also have you had time to work on the tutorial I’ve done? The email sends back to the software mail so we’ll all receive a notification if someone is interested, but I think we should stick to sending 1 PDF to test both formats and treatment. Best, Pierre Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria

1 0

Manuscript updates
by Robert Prevedel Sept. 2, 2025

Sept. 2, 2025

Dear all, thanks Pierre for implementing the latest changes in the SI, and thanks Kareem for going over the article once again. I’ve now created a new, more final, version <https://docs.google.com/document/d/1560IRCHAcZeAM2ljH5vFj6sOYo2jNNMtoUn4qpv…>, which you should all have access to. In it I deleted the old and long comment threads and accepted all changes. In the coming days I plan to take it offline to input the references - if you would like to input any more changes please do so in the new version and let me know. In the meantime, @Carlo and @Sebastian, there are still a few details highlighted in yellow that need some input from you. @Sebastian: Can you also update the Figure with the comments/changes? I think the paper can be ready by the end of week, shall we aim for another brief VC the week after to hopefully finalize? Would Thursday 11 Sept. in the afternoon work for everyone, e.g. 3pm? Best wishes, Robert -- Dr. Robert Prevedel Group Leader and Senior Scientist Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany Phone: +49 6221 387-8722 Email: robert.prevedel(a)embl.de http://www.prevedel.embl.de

1 0

Proposition of paragraph for next Newsletter
by Pierre Bouvet Sept. 1, 2025

Sept. 1, 2025

Hi everyone, Following this afternoon’s meeting, here is a proposition for a paragraph for the next newsletter: The “contact us” sends to a new email sent to “software(a)biobrillouin.org <mailto:software@biobrillouin.org>” (the address I’m sending this email to), the links to GitHub send to the two GitHub repositories. This is a “by default” version, but if you’d want to change or add things, just tell me, I’m planning on sending the newsletter on Monday. Best, Pierre PS: sorry if I was grumpy during the meeting, I’ve been trying to convince a spectrometer to work for weeks and I am starting to think it has a will of its own and that its will is entirely focused on making sure it does NOT work… I guess that’s what makes research “fun” Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria

4 7